Hi everyone! I'm trying to perform IsoNet on over 12 tomograms but due to memory and time limitations on my university's cluster i've been trouble shooting on just one tomogram. I'm able to generate star files, ctf correct, generate masks, and extract subtomos according to the tutorials and documentation successfully but when I try to run the command:
03-13 19:58:57, INFO Start Iteration1!
03-13 19:59:02, INFO Noise Level:0.0
03-13 19:59:03, ERROR multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, *kwds))
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(args))
File "/programs/x86_64-linux/isonet/0.2/IsoNet/preprocessing/prepare.py", line 126, in get_cubes
with mrcfile.open(current_mrc) as mrcData:
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/site-packages/mrcfile/load_functions.py", line 139, in open
return NewMrc(name, mode=mode, permissive=permissive,
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/site-packages/mrcfile/mrcfile.py", line 109, in init
self._open_file(name)
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/site-packages/mrcfile/mrcfile.py", line 126, in _open_file
self._iostream = open(name, self._mode + 'b')
FileNotFoundError: [Errno 2] No such file or directory: 'results/grid2U32_iter00.mrc'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/programs/x86_64-linux/isonet/0.2/IsoNet/bin/refine.py", line 114, in run
get_cubes_list(args)
File "/programs/x86_64-linux/isonet/0.2/IsoNet/preprocessing/prepare.py", line 183, in get_cubes_list
p.map(func,inp)
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'results/grid2U32_iter00.mrc'
I'm not very experienced with this type of software or python, any help would be greatly appreciated!
Hi everyone! I'm trying to perform IsoNet on over 12 tomograms but due to memory and time limitations on my university's cluster i've been trouble shooting on just one tomogram. I'm able to generate star files, ctf correct, generate masks, and extract subtomos according to the tutorials and documentation successfully but when I try to run the command:
_isonet.py refine subtomo.star --gpuID 0,1,2,3 --preprocessingncpus 16
I get this error within the log file:
03-13 19:58:47, INFO
Isonet starts refining
03-13 19:58:57, INFO Start Iteration1! 03-13 19:59:02, INFO Noise Level:0.0 03-13 19:59:03, ERROR multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/programs/x86_64-linux/isonet/0.2/IsoNet/preprocessing/prepare.py", line 126, in get_cubes with mrcfile.open(current_mrc) as mrcData: File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/site-packages/mrcfile/load_functions.py", line 139, in open return NewMrc(name, mode=mode, permissive=permissive, File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/site-packages/mrcfile/mrcfile.py", line 109, in init self._open_file(name) File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/site-packages/mrcfile/mrcfile.py", line 126, in _open_file self._iostream = open(name, self._mode + 'b') FileNotFoundError: [Errno 2] No such file or directory: 'results/grid2U32_iter00.mrc' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/programs/x86_64-linux/isonet/0.2/IsoNet/bin/refine.py", line 114, in run get_cubes_list(args) File "/programs/x86_64-linux/isonet/0.2/IsoNet/preprocessing/prepare.py", line 183, in get_cubes_list p.map(func,inp) File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/programs/x86_64-linux/isonet/0.2/miniconda/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value FileNotFoundError: [Errno 2] No such file or directory: 'results/grid2U32_iter00.mrc'
I'm not very experienced with this type of software or python, any help would be greatly appreciated!